• Briefly, EventPointer considers there is a differential splicing event if the isoforms in the associated paths change their expression in opposite directions. (bioconductor.org)
  • In other words, the identification of true orthology relationships between gene products now should progress beyond primary sequence and "splicing orthology", consisting in ancestrally shared exon-intron structures, is required to define orthologous isoforms at transcript level. (biomedcentral.com)
  • A typical human gene, then, produces multiple transcript isoforms (ten per gene, on average), that can differ both in their coding and untranslated regions. (biomedcentral.com)
  • We show that an incomplete annotation catalog can have a detrimental effect on the ability to detect differential transcript usage in transcriptomes with few isoforms per gene and that isoform-level prefiltering can considerably improve false discovery rate control. (biomedcentral.com)
  • Differences in the relative expression of these isoforms between tissues and species occur naturally between cell types and allow cells to adapt to the environment, but aberrations from this normal splicing pattern can have detrimental consequences for the organism [ 10 ]. (biomedcentral.com)
  • In particular, DTU considers changes in the proportions of the isoforms of a gene that are expressed as opposed to changes of the individual transcript levels. (biomedcentral.com)
  • A quantitative analysis of the isoforms indicated that most of the spliced genes have one major isoform and tend to simultaneously co-express a low number of isoforms, typically two, with intron retention being the most frequent alternative splicing event. (biomedcentral.com)
  • Multiple hnRNP K protein isoforms exist due to alternative splicing and display different nucleic-acid-binding properties. (bvsalud.org)
  • The 3 spliced mRNAs putatively encode good proteins , altogether 3 different isoforms (1 complete, 2 partial ), some containing a coiled coil stretch [Psort2] . (nih.gov)
  • We also characterized the RNA-Seq dataset to inventory transcript isoforms and infer alternative splicing during different stages of its development. (thecomonline.net)
  • Due to the complicated nature of the transcriptome, which comprises variable length transcripts and numerous alternatively spliced isoforms for most genes, as well as the high sequence similarity of highly abundant species of RNA, such as rRNAs, these kinds of analyses are difficult with standard short sequencing methods. (cd-genomics.com)
  • The main functionality of the DomainGraph plug-in is the visual analysis of the effects of alternative splicing on genes, protein isoforms, molecular interactions, pathways and miRNA binding sites. (g6g-softwaredirectory.com)
  • Given a gene interaction network , DomainGraph visualizes the genes together with all known encoded protein isoforms and their respective domain compositions. (g6g-softwaredirectory.com)
  • Genes, protein isoforms and domains are highlighted according to potentially occurring alternative splicing events or differential expression in different groups of samples. (g6g-softwaredirectory.com)
  • 1) Analysis of AltAnalyze Exon Array data with regard to genes, protein isoforms, pathways, and miRNA binding sites affected by alternative splicing. (g6g-softwaredirectory.com)
  • 3) Decomposition of gene interaction networks into all known encoded protein isoforms and their domain compositions. (g6g-softwaredirectory.com)
  • For a gene interaction networks , the main focus is on the encoded protein isoforms and their domain compositions. (g6g-softwaredirectory.com)
  • Thus, the genes are visualized together with all encoded isoforms and their domains. (g6g-softwaredirectory.com)
  • We investigated the predictive potential of the relative abundances of transcript isoforms for tumor staging and clinical outcome in 12 different tumor types, integrating RNA sequencing and clinical annotation data for 12 tumor types from The Cancer Genome Atlas (TCGA) project. (biorxiv.org)
  • Here's the figure showing the various predicted alternatively spliced transcripts and the various different proteins. (blogspot.com)
  • PacBio Iso-Seq data were generated for five distinct tissues to improve the functional annotation of 34,587 protein-coding genes and 42,329 transcripts. (nature.com)
  • Recent discoveries have highlighted the fact that alternative splicing and alternative transcripts are the rule, rather than the exception, in metazoan genes. (biomedcentral.com)
  • second, to provide a more detailed annotation and quantification of true human-mouse orthologous transcripts defined as transcripts of orthologous genes exhibiting the same splicing patterns. (biomedcentral.com)
  • This figure increases to 87% using less stringent criteria for gene structure similarity, thus implying that for about 13% of the human RefSeq annotated genes (and about 25% of the corresponding transcripts) we could not identify any mouse transcript showing sufficient similarity to be confidently assigned as a splicing ortholog. (biomedcentral.com)
  • The observation that alternative splicing produces large numbers of alternative transcripts and proteins, some of them conserved across species and others truly species-specific, suggests that, still maintaining the conventional definition of gene orthology, a new concept of "splicing orthology" can be defined at transcript level. (biomedcentral.com)
  • Functional and evolutionary analyses of genes are usually performed on one or few representatives of their expression products, i.e. transcripts and proteins. (biomedcentral.com)
  • From an analysis perspective, there are several ways to approach RNA-seq data to unravel differential transcript usage, such as annotation-based exon-level counting, differential analysis of the percentage spliced in, or quantitative analysis of assembled transcripts. (biomedcentral.com)
  • High-throughput sequencing of cDNA fragment populations, commonly known as RNA-seq, has rapidly become a default standard for profiling the composition of a transcriptome and quantifying the expression of individual transcriptional units (such as genes, transcripts, or exons). (biomedcentral.com)
  • However the eukaryotic transcriptome, and in particular the plant transcriptome, is far more complex than previously believed, alternative splicing and non coding transcripts being amongst the major causes contributing to this complexity. (biomedcentral.com)
  • AtRTD3 contains over 169,000 transcripts-twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. (dundee.ac.uk)
  • Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. (dundee.ac.uk)
  • Representatives of the newly identified genes and predicted alternatively spliced transcripts were experimentally validated. (thecomonline.net)
  • LncRNA-seq has opened up new and exciting research opportunities, such as (1) profiling known and novel transcripts and defining variations, (2) predicting lncRNA targeting genes, (3) distinguishing biomarkers for cancer/disease diagnostics and classification, and (4) revealing lncRNA-mRNA regulation. (cd-genomics.com)
  • On the other hand, gene expression summarizes the output of RNA transcripts from a gene locus, which is mostly explained by one transcript isoform [ 10 ]. (biorxiv.org)
  • The remaining 2 mRNA variants (1 spliced, 1 unspliced) appear not to encode good proteins. (blogspot.com)
  • Repeats in THEG (testicular haploid expressed gene) and several fly proteins. (embl-heidelberg.de)
  • When genes are active, copies of the DNA are made using molecules of ribonucleic acid (RNA) and these can then be used as templates to make proteins. (elifesciences.org)
  • Another way to control genes is by nonsense-mediated decay, where incorrect or incomplete RNA molecules are destroyed before they can be used to make defective proteins. (elifesciences.org)
  • It encodes a 136 kDa protein containing four domains present in other developmental proteins: a PWWP domain, an HMG box, a SET domain also found in the Drosophila dysmorphy gene ash -encoded protein, and a PHD-type zinc finger. (embl.de)
  • Finally, as a serendipitous finding, of the t(4;14) (p16.3;q32.3) translocations recently described in multiple myelomas, at least three breakpoints merge the IgH and WHSC1 genes, potentially causing fusion proteins replacing WHSC1 exons 1-4 by the IgH 5'-VDJ moiety. (embl.de)
  • In practice, two genes α and β are usually annotated as orthologous if their products are the "best reciprocal hits": that is, one of the proteins encoded by the α gene of species A has, as its most similar counterpart in species B, one of the proteins encoded by the β gene, and vice versa. (biomedcentral.com)
  • DNA and RNA sequencing analyses suggested that exon skipping did not result from genetic alterations in intronic or exonic cis-regulatory elements, but rather was associated with a single epigenetic modification downstream of exon 3a, and quantitative changes in the expression of trans-acting proteins that have known roles in the regulation of alternative splicing. (datadryad.org)
  • Bone cells can sense physical forces and convert mechanical stimulation conditions into biochemical signals that lead to expression of mechanically sensitive genes and proteins. (biomedcentral.com)
  • However, it is still poorly understood how genes and proteins in bone cells are orchestrated to respond to mechanical stimulations. (biomedcentral.com)
  • By carefully developing protein selection filters and statistical models, we were able to identify 42 proteins representing 21 Rat genes that were significantly associated with bone cells' response to quantitative changes between normal loading and fatigue loading conditions. (biomedcentral.com)
  • It still remains unknown what all the mechanically-sensitive genes and proteins in bone cells under mechanical stress are and how their differential expressions are regulated [ 4 ]. (biomedcentral.com)
  • Alternative splicing (AS) is the mechanism by which exons of a single gene can be spliced in various combinations to encode a diverse set of proteins. (biologists.com)
  • The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). (philarchive.org)
  • The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. (philarchive.org)
  • This study aimed to evaluate the expression levels of miR-34a and 11 of its bioinformatically selected target genes and proteins to test their potential dysregulation in RCC. (hindawi.com)
  • There are 7 probable alternative promotors and 5 non overlapping alternative last exons (see the diagram). (blogspot.com)
  • The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, overlapping exons with different boundaries, alternative splicing or retention of 4 introns. (blogspot.com)
  • The definition of splicing events by EventPointer consists in a triplet of subgraphs (P1,P2 and PR) i.e. for a cassette exon, PR correspond to the flanking exons, P1 the junctions and exon, and P2 the junction that skips the exon. (bioconductor.org)
  • The gene encoding the insect nicotinic acetylcholine receptor (nAChR) α6 subunit, target of the bio-insecticide spinosad, is one example of this and expands protein diversity via alternative splicing of mutually exclusive exons. (datadryad.org)
  • This 25 exon gene is expressed ubiquitously in early development and undergoes complex alternative splicing and differential polyadenylation. (embl.de)
  • We observed an identical exon/intron structure for 32% of human and mouse orthologous genes. (biomedcentral.com)
  • Many genes increase coding capacity by alternate exon usage. (datadryad.org)
  • Here, we show that spinosad resistance in the tomato leaf miner, Tuta absoluta is associated with aberrant regulation of splicing of Taα6 resulting in a novel form of insecticide resistance mediated by exon skipping. (datadryad.org)
  • Our results demonstrate that the intrinsic capacity of the α6 gene to generate transcript diversity via alternative splicing can be readily exploited during the evolution of resistance and identifies exon skipping as a molecular alteration conferring insecticide resistance. (datadryad.org)
  • To meet multiple research goals, we offer a complete range of arrays for whole-transcriptome-, gene-, exon-, or short noncoding (snc)RNA-level analysis. (cd-genomics.com)
  • Therefore, an in-depth analysis of Exon Array data regarding alternative splicing events and their biological impact is possible without the need of prior knowledge. (g6g-softwaredirectory.com)
  • 2) Automatic annotation and visualization of genes, Reactome (see G6G Abstract Number 20267 ) and WikiPathways (see G6G Abstract Number 20367 ), and miRNA binding sites with integrated Exon Array data. (g6g-softwaredirectory.com)
  • 9) The Hypertext Markup Language (HTML) export of AltAnalyze statistics with biological annotations (genes, pathways, miRNA binding sites, alternative exon annotations) with all gene and pathway graphics. (g6g-softwaredirectory.com)
  • Potential alternative splicing events and differential exon expression is highlighted in the network. (g6g-softwaredirectory.com)
  • I repeated my complaint that much of the predicted alternative splice variants are artifacts. (blogspot.com)
  • It makes no sense that conserved genes would be producing alternative protein variants that are species specific. (blogspot.com)
  • I am convinced that the EST databases are full of artifacts and that most predicted splice variants do not exist. (blogspot.com)
  • I asked him if he had ever looked at his favorite genes to see if the predicted variants make any sense. (blogspot.com)
  • I suggested that he look at the predicted alternative splice variants of the two human genes and let me know if he is still convinced that these variants make biological sense. (blogspot.com)
  • Down the right-hand side of the page there are links to several other webpages, including a link to AceView , a database of alternative splice variants. (blogspot.com)
  • Before following this link to the POLR1A variants, let's note that on the annotated Entrez Gene website there are no alternative splice variants listed. (blogspot.com)
  • RefSeq annotates one representative transcript (NM included in AceView variant.a), but Homo sapiens cDNA sequences in GenBank, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 11 spliced variants. (blogspot.com)
  • Alternative mRNA variants and regulation: The gene contains 29 different introns (28 gt-ag, 1 gc-ag). (blogspot.com)
  • Transcription produces 13 different mRNAs, 11 alternatively spliced variants and 2 unspliced forms. (blogspot.com)
  • Whole-genome assemblies of wild Oryza species will provide new sources of genes and gene variants/haplotypes, enhancing the ability of breeding programs to introduce desirable traits into domestic cultivars. (nature.com)
  • Since multiple transcript and protein variants expressed by the same gene are, by definition, structurally distinct and need not to be functionally equivalent, the concept of gene orthology should be extended to the transcript level in order to describe evolutionary relationships between structurally similar transcript variants. (biomedcentral.com)
  • Our data suggest that current gene and transcript data may still be rather incomplete - with several splicing variants still unknown. (biomedcentral.com)
  • Genome assembly, annotation and variant analysis - Our team are proficient in dealing with whole genome, whole-exome and targeted sequencing methods that allow for the study of genetic variants or mutations. (nottingham.ac.uk)
  • We can help researchers identify SNPs, indels, gene copy numbers, and genomic rearrangements from the various types of DNA-sequencing and microarray data and provide tailored downstream analysis of variants and mutations. (nottingham.ac.uk)
  • Alternative splicing results in multiple transcript variants. (nih.gov)
  • Canonical GT-AG and non-canonical intron variants including AT-AC introns can coexist within the same gene, potentially with an effect on gene expression due to the slow removal of U12-type introns [ 10 ]. (biomedcentral.com)
  • Variants in blood pressure genes and the risk of Accardi R, Rubino R, Scalise M et col . (2011). (who.int)
  • Transcription produces 3 alternatively spliced mRNAs . (nih.gov)
  • Here, we present a new approach for the identification of breast cancer markers that does not measure gene expression but instead uses the ratio of alternatively spliced mRNAs as its indicator. (figshare.com)
  • He is firmly convinced that most human genes express a number of different protein products that are produced as the result of alternatively spliced mRNA precursors. (blogspot.com)
  • Predicted to be involved in mRNA methylation and regulation of alternative mRNA splicing, via spliceosome. (nih.gov)
  • Predicted to act upstream of or within RNA splicing and mRNA processing. (nih.gov)
  • Eukaryotic genes are transcribed as a primary transcript that is subsequently converted to a mature mRNA through several processing steps including splicing. (biomedcentral.com)
  • Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. (nih.gov)
  • A link between AS and miRNAs was shown in 139 genes where we found that AS affects the miRNA target site. (biomedcentral.com)
  • Some miRNAs are hosted in pri-miRNAs annotated as long non-coding RNAs (lncRNAs) and defined as MIRHGs (for miRNA Host Genes). (mdpi.com)
  • circRNA-seq uncovers the molecular importance of regulating gene expression, including (1) profiling known and novel circRNAs and prediction of targeting genes, (2) categorization of biomarkers for cancer or disease diagnostics and classification, (3) discovery of regulatory networks between ncRNA and miRNA, and (4) understanding tissue or organism development mechanisms based on transcript profiles. (cd-genomics.com)
  • can be imported into DomainGraph and affected genes, pathways and miRNA binding sites are automatically annotated. (g6g-softwaredirectory.com)
  • Over the past few years, emerging numerous bioinformatic tools have been developed to identify candidate disease-causing genes [ 4 ], including microRNA (miRNA) genes. (hindawi.com)
  • An aberrant miRNA expression could contribute to cancer development and progression [ 6 , 7 ] and could affect their target genes that are involved in many biological processes, such as cell differentiation, proliferation, apoptosis, metabolism, and development [ 8 ]. (hindawi.com)
  • MicroRNA-34a gene (MIR-34A) that is located on chromosome 1p36 belongs to one of evolutionary-conserved miRNA families (MIR-34 family) that consists of three members: MIR-34A, MIR-34B, and MIR-34C [ 10 ]. (hindawi.com)
  • The software returns a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative 3',…,etc), genomic position, statistical significance and increment of the percent spliced in ( \(\Delta \Psi\) ) for all the events. (bioconductor.org)
  • Additionally, many minor introns were efficiently spliced compared to their flanking major introns. (biomedcentral.com)
  • Here we show that minor intron splicing and AS across minor introns is a highly organised process that might be regulated in coordination with the major spliceosome in a tissue-specific manner. (biomedcentral.com)
  • Splicing of introns is required for the expression of most eukaryotic genes. (biomedcentral.com)
  • In these minor intron-containing genes (MIGs), the majority of introns are usually spliced by the major spliceosome, with only one or two introns being spliced by the minor spliceosome. (biomedcentral.com)
  • Regardless, mis-splicing of these few minor introns can have detrimental consequences, as highlighted by diseases caused by mutation in minor spliceosome components. (biomedcentral.com)
  • In depth analysis of the predicted gene set revealed some errors involving genes with non-canonical splice sites in their introns. (biomedcentral.com)
  • Moreover a recent study confirmed these observations, showing that for 80% of the expressed genes in primary tissue cultures, the major transcript is expressed at a considerably higher level (at least twice) than any other isoform [ 21 ]. (biomedcentral.com)
  • Conclusions Our analyses reveal new signatures based on transcript isoform abundances that characterize tumor phenotypes and their progression independently of gene expression. (biorxiv.org)
  • We used the RNAseq data to update the existing grape gene prediction with 2,258 new coding genes and 3,336 putative long non-coding RNAs. (biomedcentral.com)
  • These results provide a simple alternative for the classification of normal and cancerous breast tumor tissues and underscore the putative role of alternative splicing in the biology of cancer. (figshare.com)
  • These findings indicate miR-34a along with its putative target genes could play a role in RCC tumorigenesis and progression. (hindawi.com)
  • My colleague is very knowledgeable about the genes for the major subunits of eukaryotic RNA polymerase since it was his lab that cloned the first one. (blogspot.com)
  • Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. (dundee.ac.uk)
  • We then sought to address specificity of MIG expression, minor intron retention, and alternative splicing (AS) across mouse and human tissues. (biomedcentral.com)
  • Our analyses revealed that intron retention is the predominant alternative splicing type in P. cubensis , with alternative 5′- and alternative 3′-splice sites occurring at lower frequencies. (thecomonline.net)
  • Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression. (wikipedia.org)
  • Expression: According to AceView, this gene is expressed at very high level, 4.8 times the average gene in this release. (blogspot.com)
  • 337 bp of this gene are antisense to spliced gene pluvu, raising the possibility of regulated alternate expression. (blogspot.com)
  • The nature of the protein motifs, the expression pattern and its mapping to the critical region led us to propose WHSC1 as a good candidate gene to be responsible for many of the phenotypic features of WHS. (embl.de)
  • Gene expression and epigenome analysis - We can assist in the study of gene expression or gene regulation. (nottingham.ac.uk)
  • Several reports have recently provided snapshots of the performance of gene-level differential expression analysis methods, using both synthetic and experimental data [ 1 - 5 ]. (biomedcentral.com)
  • 3 ] used large-scale experimental data from the SEQC (Sequencing Quality Control) consortium, consisting of replicates of well-known cell lines, to evaluate the performance of differential gene expression methods and the effects of modifying sequencing depths and the number of biological replicates. (biomedcentral.com)
  • It is important to distinguish DTU from gene-level differential expression and from transcript-level differential expression (DTE). (biomedcentral.com)
  • CD Genomics Provides high-resolution array scanning and automation to dramatically improve efficiency in gene expression. (cd-genomics.com)
  • The general workflow for gene expression Microarray is outlined below. (cd-genomics.com)
  • The encoded protein interacts with other family members to cooperatively activate gene expression. (tumorportal.org)
  • It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. (dundee.ac.uk)
  • Interestingly, biofilm formation, biofilm thickness, and the expression level of biofilm-related genes (UGD1 and UXS1) were also significantly reduced. (bvsalud.org)
  • RNA sequencing using next-generation sequencing technologies (NGS) is now the industry standard for gene expression profiling, especially in large-scale high-throughput studies. (cd-genomics.com)
  • Background Phenotypic changes during cancer progression are associated to alterations in gene expression, which can be exploited to build molecular signatures for tumor stage identification and prognosis. (biorxiv.org)
  • These signatures show similar, and sometimes better, accuracies compared with known gene expression signatures, and are largely independent of gene expression changes. (biorxiv.org)
  • Although tumors originate primarily from genetic lesions, their progression involves other molecular transformations, which are related to the activation of specific aggressive phenotypes, like tumor spread and metastasis, and are often reflected in gene expression changes [ 4 , 5 ]. (biorxiv.org)
  • Accordingly, the development of gene expression signatures has been instrumental to complement and improve stage identification and prognosis [ 6 - 9 ]. (biorxiv.org)
  • Our analyses revealed new signatures that characterize tumor phenotypes and their progression largely independent of gene expression. (biorxiv.org)
  • This class of noncoding RNAs is small, single stranded, and 19-25 nucleotide long that act as negative regulators involved in posttranscriptional silencing of the gene expression [ 5 ]. (hindawi.com)
  • Our data have provided evidence for a comparable prediction of clinical outcome in CMF-treated breast cancer patients using conventional clinical variables and gene expression based markers. (lu.se)
  • AceView: gene:dpy-21, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView. (nih.gov)
  • The sequence of this gene is defined by 537 GenBank accessions from 518 cDNA clones, some from breast (seen 40 times), marrow (29), head neck (19), brain (18), eye (18), leukopheresis (18), lung tumor (18) and 132 other tissues. (blogspot.com)
  • Here we describe a detailed survey of alternative splicing in grape based on 124 SOLiD RNAseq analyses from different tissues, stress conditions and genotypes. (biomedcentral.com)
  • Using a high-throughput reverse transcription-PCR-based system for splicing annotation, we monitored the alternative splicing profiles of 600 cancer-associated genes in a panel of 21 normal and 26 cancerous breast tissues. (figshare.com)
  • We validated 41 alternative splicing events that significantly differed in breast tumors relative to normal breast tissues. (figshare.com)
  • In a blind screen, a classifier based on the 12 best cancer-associated splicing events correctly identified cancer tissues with 96% accuracy. (figshare.com)
  • Moreover, a subset of these alternative splicing events could order tissues according to histopathologic grade, and 5 markers were validated in a further blind set of 19 grade 1 and 19 grade 3 tumor samples. (figshare.com)
  • This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones. (nih.gov)
  • Genes are sequences of DNA that contain instructions for the cell that must be carefully controlled because it is not always appropriate or safe for these instructions to be followed. (elifesciences.org)
  • Each RBH couple consists of two genes, one from each of the two genome sequences (or genomes) to compare, which display the highest scoring hit in the other data set in a reciprocal manner [ 36 ]. (biomedcentral.com)
  • The protein encoded by this gene interacts with the transcription factor myocardin, a key regulator of smooth muscle cell differentiation. (nih.gov)
  • This gene encodes a member of the D subfamily of sex determining region y-related transcription factors that are characterized by a conserved DNA-binding domain termed the high mobility group box and by their ability to bind the minor groove of DNA. (tumorportal.org)
  • We develop novel methods to determine splice junctions and transcription start and end sites accurately. (dundee.ac.uk)
  • The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species. (dundee.ac.uk)
  • The sequence of this gene is defined by 16 cDNA clones and 18 elements defined by RNA-seq, some from mixed (seen 7 times), embryo (5), l2 (once). (nih.gov)
  • We tried several gene selection strategies, and built classifiers using the resulting cDNA microarray gene lists. (lu.se)
  • Given that the minor spliceosome is ubiquitously expressed, we hypothesized that these restricted phenotypes might be caused by the tissue-specific regulation of the minor spliceosome targets, i.e. minor intron-containing genes (MIGs). (biomedcentral.com)
  • One way to explain this paradox of systemic minor spliceosome inhibition resulting in tissue-specific phenotypes would be that the MIGs are expressed, spliced and/or alternatively spliced in a tissue-specific manner. (biomedcentral.com)
  • Two of the subunits, Rpb1 and Rbp2, are more commonly known as A and B. In the human genome they are encoded by the genes POLR2A and POLR2B respectively [ RNA Polymerase Genes in the Human Genome ]. (blogspot.com)
  • The corresponding genes for the DFS-SEs were significantly enriched in mitochondria and their associated pathways according to Gene Ontology annotation and in the pathways of fatty acid metabolism, oxidative phosphorylation and Huntington's disease according to a Kyoto Encyclopedia of Genes and Genomes pathway analysis. (spandidos-publications.com)
  • Since non-canonical splice sites are difficult to predict ab initio, we checked for options to improve the annotation by transferring annotation information from the recently released Columbia-0 reference genome sequence annotation Araport11. (biomedcentral.com)
  • The improved gene set of the Nd-1 genome assembly (GeneSet_Nd-1_v1.1) was evaluated via comparison to the initial gene prediction (GeneSet_Nd-1_v1.0) as well as against Araport11 for the Col-0 reference genome sequence. (biomedcentral.com)
  • RNA-Seq data ("external hints") does not support the detection and annotation of non-canonical splice sites on genome sequence assemblies at a satisfying level [ 26 , 27 , 28 ]. (biomedcentral.com)
  • Furthermore, full-length transcript sequence data is extremely useful for genome annotation and gene function research. (cd-genomics.com)
  • Our expertise in dealing with both shotgun and high throughput sequencing data can empower researchers with accurate gene prediction and precise species categorisation. (nottingham.ac.uk)
  • Incorporation of hints generated from Araport11 enabled the precise prediction of non-canonical splice sites. (biomedcentral.com)
  • Reciprocal best hits for 24,527 (89.4%) of all nuclear Col-0 genes against the GeneSet_Nd-1_v1.1 indicate a high gene prediction quality. (biomedcentral.com)
  • Despite attempts to annotate non-canonical splice sites automatically [ 24 , 25 ], ab initio gene prediction without experimental support from e.g. (biomedcentral.com)
  • Alternative splicing, chromosome assignment and subcellular localizationof the testicular haploid expressed gene (THEG). (embl-heidelberg.de)
  • Since U4atac snRNA is ubiquitously expressed, mutation in this gene is expected to result in systemic inhibition of the minor spliceosome. (biomedcentral.com)
  • It's not a surprise that the Entrez Gene annotators have ignored these predictions. (blogspot.com)
  • Thus, it has been proposed that the complexity of higher metazoans must arise via the regulation of these genes at the transcriptional and post-transcriptional level. (biologists.com)
  • Its main contribution is a statistical analysis based on the Poisson-Binomial (PB) distribution to take into account the mutation rate of genes and samples. (unav.edu)
  • Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm. (bioconductor.org)
  • We always advise our clients on the potential alternative uses of data in order to ensure a maximum return on their investments. (nottingham.ac.uk)
  • In the present study, the data of splicing events and the clinical information of PRAD patients were obtained from The Cancer Genome Atlas (TCGA)SpliceSeq and TCGA databases, respectively. (spandidos-publications.com)
  • Single Experiment Data - This option can be used to analyze, e.g. a single tissue with regard to potentially occurring alternative splicing events. (g6g-softwaredirectory.com)
  • Alternative splicing is the primary mechanism by which a limited number of protein-coding genes can generate proteome diversity. (biologists.com)